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A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies

Junha Shin, Harald Marx, Alicia Richards, Dries Vaneechoutte, Dhileepkumar Jayaraman, Junko Maeda, Sanhita Chakraborty, Michael Sussman, Klaas Vandepoele (UGent) , Jean-Michel Ané, et al.
(2021) NUCLEIC ACIDS RESEARCH. 49(1).
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Abstract
Comparative functional genomics offers a powerful approach to study species evolution. To date, the majority of these studies have focused on the transcriptome in mammalian and yeast phylogenies. Here, we present a novel multi-species proteomic dataset and a computational pipeline to systematically compare the protein levels across multiple plant species. Globally we find that protein levels diverge according to phylogenetic distance but is more constrained than the mRNA level. Module-level comparative analysis of groups of proteins shows that proteins that are more highly expressed tend to be more conserved. To interpret the evolutionary patterns of conservation and divergence, we develop a novel network-based integrative analysis pipeline that combines publicly available transcriptomic datasets to define co-expression modules. Our analysis pipeline can be used to relate the changes in protein levels to different species-specific phenotypic traits. We present a case study with the rhizobia-legume symbiosis process that supports the role of autophagy in this symbiotic association.
Keywords
Genetics, SACCHAROMYCES-CEREVISIAE, EXPRESSION LEVELS, GENE DUPLICATION, EVOLUTION, REVEALS, ANNOTATION, ONTOLOGY, GENOMES, CYCLE

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MLA
Shin, Junha, et al. “A Network-Based Comparative Framework to Study Conservation and Divergence of Proteomes in Plant Phylogenies.” NUCLEIC ACIDS RESEARCH, vol. 49, no. 1, 2021, doi:10.1093/nar/gkaa1041.
APA
Shin, J., Marx, H., Richards, A., Vaneechoutte, D., Jayaraman, D., Maeda, J., … Roy, S. (2021). A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies. NUCLEIC ACIDS RESEARCH, 49(1). https://doi.org/10.1093/nar/gkaa1041
Chicago author-date
Shin, Junha, Harald Marx, Alicia Richards, Dries Vaneechoutte, Dhileepkumar Jayaraman, Junko Maeda, Sanhita Chakraborty, et al. 2021. “A Network-Based Comparative Framework to Study Conservation and Divergence of Proteomes in Plant Phylogenies.” NUCLEIC ACIDS RESEARCH 49 (1). https://doi.org/10.1093/nar/gkaa1041.
Chicago author-date (all authors)
Shin, Junha, Harald Marx, Alicia Richards, Dries Vaneechoutte, Dhileepkumar Jayaraman, Junko Maeda, Sanhita Chakraborty, Michael Sussman, Klaas Vandepoele, Jean-Michel Ané, Joshua Coon, and Sushmita Roy. 2021. “A Network-Based Comparative Framework to Study Conservation and Divergence of Proteomes in Plant Phylogenies.” NUCLEIC ACIDS RESEARCH 49 (1). doi:10.1093/nar/gkaa1041.
Vancouver
1.
Shin J, Marx H, Richards A, Vaneechoutte D, Jayaraman D, Maeda J, et al. A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies. NUCLEIC ACIDS RESEARCH. 2021;49(1).
IEEE
[1]
J. Shin et al., “A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies,” NUCLEIC ACIDS RESEARCH, vol. 49, no. 1, 2021.
@article{8683544,
  abstract     = {{Comparative functional genomics offers a powerful approach to study species evolution. To date, the majority of these studies have focused on the transcriptome in mammalian and yeast phylogenies. Here, we present a novel multi-species proteomic dataset and a computational pipeline to systematically compare the protein levels across multiple plant species. Globally we find that protein levels diverge according to phylogenetic distance but is more constrained than the mRNA level. Module-level comparative analysis of groups of proteins shows that proteins that are more highly expressed tend to be more conserved. To interpret the evolutionary patterns of conservation and divergence, we develop a novel network-based integrative analysis pipeline that combines publicly available transcriptomic datasets to define co-expression modules. Our analysis pipeline can be used to relate the changes in protein levels to different species-specific phenotypic traits. We present a case study with the rhizobia-legume symbiosis process that supports the role of autophagy in this symbiotic association.}},
  articleno    = {{e3}},
  author       = {{Shin, Junha and Marx, Harald and Richards, Alicia and Vaneechoutte, Dries and Jayaraman, Dhileepkumar and Maeda, Junko and Chakraborty, Sanhita and Sussman, Michael and Vandepoele, Klaas and Ané, Jean-Michel and Coon, Joshua and Roy, Sushmita}},
  issn         = {{0305-1048}},
  journal      = {{NUCLEIC ACIDS RESEARCH}},
  keywords     = {{Genetics,SACCHAROMYCES-CEREVISIAE,EXPRESSION LEVELS,GENE DUPLICATION,EVOLUTION,REVEALS,ANNOTATION,ONTOLOGY,GENOMES,CYCLE}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{23}},
  title        = {{A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies}},
  url          = {{http://dx.doi.org/10.1093/nar/gkaa1041}},
  volume       = {{49}},
  year         = {{2021}},
}
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